densityTree: Plots a posterior sample of trees
In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

densityTree

R Documentation

Plots a posterior sample of trees

Description

Functions plots a posterior sample of trees, including with mapped discrete characters.

make.transparent is used internally and converts a color to transparent with a certain user-specified alpha level.

Usage

densityTree(trees, colors="blue", alpha=NULL, method="plotTree", 
   fix.depth=FALSE, use.edge.length=TRUE, compute.consensus=TRUE, 
   use.gradient=FALSE, show.axis=TRUE, ...)
make.transparent(color, alpha)

Arguments

`trees`	an object of class `"multiPhylo"` or `"multiSimmap"`.
`colors`	a color or a named vector of colors in which names correspond to mapped states in an object of class `"multiSimmap"`.
`alpha`	transparency level for plotted trees which is passed to internally used function, `make.transparent`. (`0` is fully transparent, which `1` is fully opaque.) By default will be one divided by the number of trees.
`method`	plotting method to be used internally. Can be `"plotTree"` or `"plotSimmap"`.
`fix.depth`	logical value indicating whether or not to plot trees with a fixed depth or to permit plotted trees to have different depths.
`use.edge.length`	logical value indicating whether to use the edge lengths of the input tree. Defaults to `use.edge.length=TRUE` unless any input tree edge lengths are `NULL`.
`compute.consensus`	logical value indicating whether or not to use the tip order from a consensus tree. (Defaults to `compute.consensus=TRUE` Defaulted to `FALSE` in earlier version of this function.)
`use.gradient`	logical value indicating whether to plot all trees slightly offset using a rainbow color gradient. (Defaults to `use.gradient=FALSE`.)
`show.axis`	logical value indicating whether or not to include a horizontal axis in the plot.
`...`	arguments to be passed to `plotTree` or `plotSimmap`. Some may be ignored if they are incompatible with the method.
`color`	in `make.transparent`, the color (or colors in a vector) to render transparent.